ArticleInternational journal of molecular sciences2019
Molecular Network-Based Drug Prediction in Thyroid Cancer.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it, 20 citations in OpenAlex.
- RUNX3 Expression Level Is Correlated with the Clinical and Pathological Characteristics in Endometrial Cancer: A Systematic Review and Meta-analysis.BioMed research international · 2021Pooled it
- Investigating the potential anti-cancer mechanism for thyroid cancer: Role of Herba Epimedii via network pharmacology approach.Journal, genetic engineering & biotechnology · 2025Article
- Drug Repositioning Based on Deep Sparse Autoencoder and Drug-Disease Similarity.Interdisciplinary sciences, computational life sciences · 2024Article
- Analysis of Human Papillomavirus-Associated Cervical Cancer Differentially Expressed Genes and Identification of Prognostic Factors using Integrated Bioinformatics Approaches.Advanced biomedical research · 2024Article
- Drug repositioning in thyroid cancer treatment: the intriguing case of anti-diabetic drugs.Frontiers in pharmacology · 2023Review
- Computational drug repositioning using similarity constrained weight regularization matrix factorization: A case of COVID-19.Journal of cellular and molecular medicine · 2022Article
- A Computational Framework to Identify Transcriptional and Network Differences between Hepatocellular Carcinoma and Normal Liver Tissue and Their Applications in Repositioning Drugs.BioMed research international · 2021Article
- Agent Repurposing for the Treatment of Advanced Stage Diffuse Large B-Cell Lymphoma Based on Gene Expression and Network Perturbation Analysis.Frontiers in genetics · 2021Article
- A Computational Framework to Identify Biomarkers for Glioma Recurrence and Potential Drugs Targeting Them.Frontiers in genetics · 2021Article
- Bioinformatics Analysis RevealsComputational and mathematical methods in medicine · 2021Article
- Identification of Potential BRAF Inhibitor Joint Therapy Targets in PTC based on WGCAN and DCGA.Journal of Cancer · 2021Article
- A Review of CurrentFrontiers in oncology · 2021Review
- Application of Circulating Tumor DNA as a Biomarker for Non-Small Cell Lung Cancer.Frontiers in oncology · 2021Review
- Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression.International journal of molecular sciences · 2020Review
- Computational Models in Non-Coding RNA and Human Disease.International journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As a common malignant tumor disease, thyroid cancer lacks effective preventive and therapeutic drugs. Thus, it is crucial to provide an effective drug selection method for thyroid cancer patients. The connectivity map (CMAP) project provides an experimental validated strategy to repurpose and optimize cancer drugs, the rationale behind which is to select drugs to reverse the gene expression variations induced by cancer. However, it has a few limitations. Firstly, CMAP was performed on cell lines, which are usually different from human tissues. Secondly, only gene expression information was considered, while the information about gene regulations and modules/pathways was more or less ignored. In this study, we first measured comprehensively the perturbations of thyroid cancer on a patient including variations at gene expression level, gene co-expression level and gene module level. After that, we provided a drug selection pipeline to reverse the perturbations based on drug signatures derived from tissue studies. We applied the analyses pipeline to the cancer genome atlas (TCGA) thyroid cancer data consisting of 56 normal and 500 cancer samples. As a result, we obtained 812 up-regulated and 213 down-regulated genes, whose functions are significantly enriched in extracellular matrix and receptor localization to synapses. In addition, a total of 33,778 significant differentiated co-expressed gene pairs were found, which form a larger module associated with impaired immune function and low immunity. Finally, we predicted drugs and gene perturbations that could reverse the gene expression and co-expression changes incurred by the development of thyroid cancer through the Fisher's exact test. Top predicted drugs included validated drugs like baclofen, nevirapine, glucocorticoid, formaldehyde and so on. Combining our analyses with literature mining, we inferred that the regulation of thyroid hormone secretion might be closely related to the inhibition of the proliferation of thyroid cancer cells.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.